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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
Abstract
Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first-principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested. Catalytically relevant fields calculated with AMOEBA were typically smaller than those observed with additive potentials, but were generally consistent with an electrostatically driven mechanism for catalysis. Our results highlight the accuracy and the potential advantages of using polarizable force fields in systems where accurate electrostatics may be crucial for providing mechanistic insights.
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Authors (4)
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Richard Bradshaw
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Chris-Kriton Skylaris
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Jonathan Essex
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Full text
- Publication version
- Accepted or Published Version
- DOI:
- Digital Object Identifier (open in new tab) 10.1021/acs.jcim.0c00217
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Details
- Category:
- Articles
- Type:
- artykuły w czasopismach
- Published in:
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Journal of Chemical Information and Modeling
no. 60,
pages 3131 - 3144,
ISSN: 1549-9596 - Language:
- English
- Publication year:
- 2020
- Bibliographic description:
- Bradshaw R., Dziedzic J., Skylaris C., Essex J.: The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?// Journal of Chemical Information and Modeling -Vol. 60,iss. 6 (2020), s.3131-3144
- DOI:
- Digital Object Identifier (open in new tab) 10.1021/acs.jcim.0c00217
- Verified by:
- Gdańsk University of Technology
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